rs1205336

Variant names:

• chr20-34338530-G-A
• rs1205336
• ENST00000743410.1:n.79-20651C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-34338530-G-A
• chr20-34338530-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000743410.1(ENSG00000296893):​n.79-20651C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,018 control chromosomes in the GnomAD database, including 19,754 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (19754 hom., cov: 32)
• Consequence: ENSG00000296893 ENST00000743410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 6 publications found

Genes affected

ENSG00000296893 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296893	ENST00000743410.1	n.79-20651C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76900 AN: 151900 Hom.: 19736 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.504

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.506 AC: 76952 AN: 152018 Hom.: 19754 Cov.: 32 AF XY: 0.503 AC XY: 37377 AN XY: 74290

African (AFR) AF: 0.506 AC: 20997 AN: 41472

American (AMR) AF: 0.622 AC: 9493 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3109 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2614 AN: 4828

European-Finnish (FIN) AF: 0.398 AC: 4197 AN: 10536

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33431 AN: 67978

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.471 Hom.: 2068

Bravo AF: 0.524

Asia WGS AF: 0.565 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.70
PhyloP100		-0.047

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1205336; hg19: chr20-32926336;